Narita Airport will be the entry point to Japan for many. Practically all international flights go through Narita. The airport is located 60km from central Tokyo.
The airport has 2 large terminals, with the first terminal divided in a North and South wing. Each terminal has their other train station and shuttle bus services are available between the two terminals.
When you lend here, it's the usual procedure, going through immigration (which now includes a fingerprint scan and simple head shot), then get your suitcase(s) and then through customs. They usually ask for you to open your suitcase and ask a few questions. I must say the officials at customs here are VERY friendly and helpful. After this, you've finally arrived in Japan!